readtree.h

   1 #ifndef READTREE_H
   2 #define READTREE_H
   3 /*
   4  *  readtree.h
   5  *  Mothur
   6  *
   7  *  Created by Sarah Westcott on 1/22/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12 using namespace std;
  13
  14 #include "mothur.h"
  15 #include "globaldata.hpp"
  16 #include "tree.h"
  17
  18 #define MAX_LINE                513
  19 #define SKIPLINE(f,c)   {while((c=f.get())!=EOF && ((c) != '\n')){}}
  20
  21 class Tree;
  22
  23 /****************************************************************************/
  24
  25 class ReadTree {
  26         public:
  27                 ReadTree();
  28                 ~ReadTree() {};
  29
  30                 virtual int read() = 0;
  31                 int readSpecialChar(istream&, char, string);
  32                 int readNodeChar(istream& f);
  33                 float readBranchLength(istream& f);
  34
  35         protected:
  36                 GlobalData* globaldata;
  37                 int numNodes, numLeaves;
  38
  39
  40 };
  41
  42 /****************************************************************************/
  43
  44 class ReadNewickTree : public ReadTree {
  45
  46 public:
  47         ReadNewickTree(string file) : treeFile(file) { openInputFile(file, filehandle); readOk = 0; }
  48         ~ReadNewickTree() {};
  49         int read();
  50
  51 private:
  52         Tree* T;
  53         int readNewickInt(istream&, int&, Tree*);
  54         int readTreeString();
  55         void nexusTranslation();
  56         ifstream filehandle;
  57         string treeFile;
  58         string holder;
  59         int readOk;  // readOk = 0 means success, readOk = 1 means errors.
  60
  61 };
  62
  63 /****************************************************************************/
  64
  65 #endif